The current GATK version is 3.2-2

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Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

Posts: 1Member
edited January 2013

Hi, I want to run GATK in Galaxy and the required version is 1.4. Can you tell me where I can download this from? I've got the source for version 1.4 from github, so I can build it if need be, but I was wondering if there's a repository for older binaries. Many thanks, Graham

Post edited by Geraldine_VdAuwera on
Tagged:

Hi Graham, No, we don't provide older binaries, you'll need to compile your own. Note that we strongly recommend using more recent versions, as older versions have bugs that have been fixed in the newer... Good luck!

Geraldine Van der Auwera, PhD

Oops, correction -- we do have the old binaries, they're on our public FTP server.

Geraldine Van der Auwera, PhD

And another correction -- they're in a private dir on the ftp, so I've copied the most relevant ones to our public dropbox here: https://www.dropbox.com/sh/1misjysdehceq4h/GnQB948vMl

Geraldine Van der Auwera, PhD

• Posts: 1Member

I tried version 1.6-13-g91f02df in Galaxy and it works fine, at least for the tools I have tested.

• Posts: 2Member

Can I get the GATK version 2.0 but before 2.4? I want to use the somaticindeldetector. Thanks!

Hi @Tgong,

Geraldine Van der Auwera, PhD

• Posts: 1Member

so i have NO idea t all how to get the binary for gatk 2.3.9 from the source code....sigh the inconvenience of not being familiar with java... anyway.... can anyone help me out here and post the binary for 2.3.9? i need t use somatic indel detector

edited May 2013

Hi @arkal,

It's actually really easy to build from source, you should give it a try -- you will feel empowered for future work!

2. From your terminal/console, navigate to the directory containing the source code. There, you run the command:

ant clean dist

This will do everything for you. The compiled binary will be in the newly-created dist directory.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

• University of PennsylvaniaPosts: 23Member

Greetings!

I tried doing this for GATK v2.2 and the error message said "Buildfile: build.xml does not exist!" even though I see it in the directory. Am I missing something?

Thanks! Stephanie

• University of PennsylvaniaPosts: 23Member

Sorry, nevermind, it works when one is logged into the node.

Greetings, Stephanie, and glad it's working for you now :)

Geraldine Van der Auwera, PhD

• University of PennsylvaniaPosts: 23Member

Thanks Geraldine!

But I have another question. I'm running GATK v2.2 on whole genome data aligned to hg19. In the very first GATK step, the output log file has this in the header:

"WARN 13:11:21,653 VCFStandardHeaderLines\$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but standard is A -- descriptions disagree; header has 'Allele Frequency' but standard is 'Allele Frequency, for each ALT allele, in the same order as listed' INFO 13:11:21,657 RMDTrackBuilder - Loading Tribble index from disk for file /gpfs/fs121/h/stechen/reference_files/sorted_dbsnp_132.hg19.vcf "

But it seems to still run. Is that okay?

Thanks! Stephanie